I am running Trinity on a high-mem/multi CPU server and am getting a large number of out-of memory errors in the butterfly step, the machine has 2TB of RAM and 143 CPU's.
This is how I am invoking Trinity:
$TRINITYCMD --trimmomatic --SS_lib_type RF --seqType fq --max_memory 1500G --left $1 --right $2 --CPU 140 --output ./Trinity-trimmomatic
As a work-around, I have to re-run the pipeline with lower CPU settings, sometimes several times, to clean up the remaining jobs, but that does not seem like the best way of handling it.
The errors I am getting look like out of memory, which is strange given the machine has 2TB of RAM:
We are sorry, commands in file: [failed_butterfly_commands.8603.txt] failed. :-( Error occurred during initialization of VM java.lang.OutOfMemoryError: unable to create new native thread ... Error, cmd: /net/apps/cbu/stow/trinityrnaseq-Trinity-v2.4.0/trinity-plugins/parafly/bin/ParaFly -c recursive_trinity.cmds -CPU 140 -v died with ret 256 at /net/apps/cbu/stow/trinityrnaseq-Trinity-v2.4.0/Trinity line 2462.
## this is the txt file:
java -Xmx4G -Xms1G -Xss1G -XX:ParallelGCThreads=2 -jar /net/apps/cbu/stow/trinityrnaseq-Trinity-v2.4.0/Butterfly/Butterfly.jar -N 100000 -L 200 -F 500 -C /export/jonassenfs/michaeld/licebase/genomedata/Halicryptus_spinulosus/Trinity-trimmomatic/read_partitions/Fb_0/CBin_863/c86329.trinity.reads.fa.out/chrysalis/Component_bins/Cbin0/c2.graph --path_reinforcement_distance=25